GSE157329 - Update for earlyHumanEmbryogenesisAtlas

[arschat]

Contributor message:

I am one of the authors on the publication of the dataset. The dataset was originally submitted to GEO (GSE157329) and have updated since. We did not submit it to HCA but it appears on HCA and causes some confusion. I found the “description” and deposited files on HCA were still from the old version. I have received several inquiries on the inconsistency. Could you please update the dataset on HCA to keep it consistent with GSE157329? Thank you so much.

Project short name:

earlyHumanEmbryogenesisAtlas

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: pre-print - 10.1038/s41556-023-01108-w

• Accessioned data: GSE157329 ingest

Key Events

• [ ] Convert published metadata to HCA spreadsheet
• [ ] Manually curate dataset to meet HCA metadata standard
• [ ] Collect any matrix and cell-type annotation files
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• [ ] Upload sheet to validate metadata
• [ ] Transfer raw files to ingest to validate data files
• [ ] Check linking using ingest graph validator
• [ ] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [ ] Submit dataset to Production
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[arschat]

Will's message on handover:

GSE157329 - Contributor messaged asking us to update

• Metadata spreadsheet
• File comparison
• Upload area - 28337cd9-688c-463d-ad00-68a7546569fe

[arschat]

email from contributor here

[arschat]

Changes from previous submission:

• gestational age did not match the according carnegie stage. it is likely that 14 days have not been added to the post ovulation age.
• analysis file "GSE157329_cell_annotate.csv.gz" contains same sample_IDs that do not match the GEO title. We are going to use those sample_ID for specimen_id and the GEO title for cs_id.
• almost half of previous specimens and cell_suspensions, have updated info. We need to decide if we still want to keep the UUIDs, or create a new submission

[arschat]

Similarly with #1152 we need to do an update in a published project to add more files (or biomaterials). Current option is using Enrique's script to populate a new submission with previous uuids & metadata. New entities will have to have a new uuid. Waiting to discuss this on ops call.

[arschat]

We will discuss how to deal with multiple submission in hca roadmap call friday 18th.

[arschat]

In the ops call we discussed the option to generate a mapping json manually for the submission uuid filling. @arschat to continue comment

[arschat]

manual mapping done global_uuid_mapping.json

[arschat]

Updating uuids with script is done.

[arschat]

• [x] graph valid
• [x] exported
• [x] import form sent